Support for datetime calculations in cohort definitions

src/main/java/org/ohdsi/circe/check/checkers/Comparisons.java

@@ -23,18 +23,16 @@
 import java.util.*;
 import java.util.function.Predicate;
 import java.util.stream.Collectors;
-
 import org.apache.commons.lang3.builder.EqualsBuilder;
 import org.ohdsi.circe.cohortdefinition.*;
 import org.ohdsi.circe.vocabulary.Concept;
 
 public class Comparisons {
-
-    private static final Map<String, Integer> TIME_UNIT_CONVERSION = new HashMap<>();
-    static {
-        TIME_UNIT_CONVERSION.put(IntervalUnit.HOUR.getName(), 60 * 60);
-        TIME_UNIT_CONVERSION.put(IntervalUnit.MINUTE.getName(), 60);
-    }
+  private static final Map<String, Integer> TIME_UNIT_CONVERSION = new HashMap<>();
+  static {
+    TIME_UNIT_CONVERSION.put(IntervalUnit.HOUR.getName(), 60 * 60);
+    TIME_UNIT_CONVERSION.put(IntervalUnit.MINUTE.getName(), 60);
+  }
 
     public static Boolean startIsGreaterThanEnd(NumericRange r) {
 
@@ -120,13 +118,14 @@ public static int compareTo(ObservationFilter filter, Window window) {
     }
     return range1 - (range2End - range2Start);
   }
-    private static int getTimeInSeconds(Window.Endpoint endpoint) {
-        return Optional.ofNullable(endpoint)
-                .map(ep -> {
-                    int convertRate = TIME_UNIT_CONVERSION.getOrDefault(ep.timeUnit, 1);
-                    return Objects.nonNull(ep.timeUnitValue) ? ep.coeff * ep.timeUnitValue * convertRate : 0;
-                }).orElse(0);
-        }
+  private static int getTimeInSeconds(Window.Endpoint endpoint) {
+    return Optional.ofNullable(endpoint)
+      .map(ep -> {
+        int convertRate = TIME_UNIT_CONVERSION.getOrDefault(ep.timeUnit, 1);
+        return Objects.nonNull(ep.timeUnitValue) ? ep.coeff * ep.timeUnitValue * convertRate : 0;
+      }).orElse(0);
+  }
+
 
     public static boolean compare(Criteria c1, Criteria c2) {
 

src/main/java/org/ohdsi/circe/check/checkers/ExitCriteriaDaysOffsetCheck.java

@@ -18,17 +18,14 @@
 
 package org.ohdsi.circe.check.checkers;
 
+import static org.ohdsi.circe.check.operations.Operations.match;
+import static org.ohdsi.circe.cohortdefinition.DateOffsetStrategy.DateField.StartDate;
+
+import java.util.Objects;
 import org.ohdsi.circe.check.WarningSeverity;
 import org.ohdsi.circe.cohortdefinition.CohortExpression;
 import org.ohdsi.circe.cohortdefinition.DateOffsetStrategy;
 
-import java.util.Arrays;
-import java.util.List;
-import java.util.Objects;
-
-import static org.ohdsi.circe.check.operations.Operations.match;
-import static org.ohdsi.circe.cohortdefinition.DateOffsetStrategy.DateField.StartDate;
-
 public class ExitCriteriaDaysOffsetCheck extends BaseCheck {
 
     private static final String DAYS_OFFSET_WARNING = "Cohort Exit criteria: %ss offset from start date should be greater than 0";
@@ -43,9 +40,9 @@ protected WarningSeverity defineSeverity() {
     protected void check(CohortExpression expression, WarningReporter reporter) {
 
         match(expression.endStrategy)
-            .isA(DateOffsetStrategy.class)
-            .then(s -> match((DateOffsetStrategy)s)
-                .when(dateOffsetStrategy -> Objects.equals(StartDate, dateOffsetStrategy.dateField) &&  0 == dateOffsetStrategy.offsetUnitValue)
-                .then(dateOffsetStrategy -> reporter.add(String.format(DAYS_OFFSET_WARNING, dateOffsetStrategy.offsetUnit))));
+                .isA(DateOffsetStrategy.class)
+                .then(s -> match((DateOffsetStrategy)s)
+                  .when(dateOffsetStrategy -> Objects.equals(StartDate, dateOffsetStrategy.dateField) &&  (0 == dateOffsetStrategy.offsetUnitValue || 0 == dateOffsetStrategy.offset))
+                  .then(dateOffsetStrategy -> reporter.add(String.format(DAYS_OFFSET_WARNING, dateOffsetStrategy.offsetUnit))));
     }
 }

src/main/java/org/ohdsi/circe/check/checkers/FirstTimeInHistoryCheck.java

@@ -42,10 +42,10 @@ protected void checkCriteria(CorelatedCriteria criteria, String groupName, Warni
         String name = CriteriaNameHelper.getCriteriaName(criteria.criteria) + " at " + groupName;
         Execution addWarning = () -> reporter.add(WARNING, name);
         match(criteria)
-            .when(c -> c.startWindow != null && ((c.startWindow.start != null && c.startWindow.start.days  != null)
-                || (c.startWindow.end != null && c.startWindow.end.days  != null))
-                || c.startWindow != null && (( c.startWindow.start != null && c.startWindow.start.timeUnitValue != null)
-                || (c.startWindow.end != null) && c.startWindow.end.timeUnitValue != null))
+                .when(c -> c.startWindow != null && ((c.startWindow.start != null && c.startWindow.start.days != null)
+                        || (c.startWindow.end != null && c.startWindow.end.days != null))
+                        || c.startWindow != null && ((c.startWindow.start != null && c.startWindow.start.timeUnitValue != null)
+                        || (c.startWindow.end != null) && c.startWindow.end.timeUnitValue != null))
                 .then(cc -> match(cc.criteria)
                         .isA(ConditionEra.class)
                         .then(c -> match((ConditionEra)c)

src/main/java/org/ohdsi/circe/check/checkers/RangeCheck.java

@@ -25,7 +25,6 @@
 import org.ohdsi.circe.cohortdefinition.Window;
 
 import java.util.Objects;
-import java.util.Optional;
 
 public class RangeCheck extends BaseValueCheck {
     private static final String NEGATIVE_VALUE_ERROR = "Time window in criteria \"%s\" has negative value %d at %s";
@@ -52,25 +51,25 @@ protected void checkInclusionRules(final CohortExpression expression, WarningRep
         }
     }
 
-    private void checkWindow(Window window, WarningReporter reporter, String name) {
-        if (Objects.isNull(window)) {
-            return;
-        }
-        checkAndReportIfNegative(window.start, reporter, name, "start");
-        checkAndReportIfNegative(window.end, reporter, name, "end");
+  private void checkWindow(Window window, WarningReporter reporter, String name) {
 
+    if (Objects.isNull(window)) {
+      return;
     }
+    checkAndReportIfNegative(window.start, reporter, name, "start");
+    checkAndReportIfNegative(window.end, reporter, name, "end");
+  }
 
-    private void checkAndReportIfNegative(Window.Endpoint windowDetails, WarningReporter reporter, String name, String type) {
-        if (Objects.nonNull(windowDetails) && Objects.nonNull(windowDetails.days) && windowDetails.days < 0) {
-            reporter.add(NEGATIVE_VALUE_ERROR, name, windowDetails.days, type);
-        } else if (Objects.nonNull(windowDetails) && Objects.nonNull(windowDetails.timeUnitValue) && windowDetails.timeUnitValue < 0) {
-            reporter.add(NEGATIVE_VALUE_ERROR, name, windowDetails.timeUnitValue, type);
-        }
+  private void checkAndReportIfNegative(Window.Endpoint windowDetails, WarningReporter reporter, String name, String type) {
+    if (Objects.nonNull(windowDetails) && Objects.nonNull(windowDetails.days) && windowDetails.days < 0) {
+      reporter.add(NEGATIVE_VALUE_ERROR, name, windowDetails.days, type);
+    } else if (Objects.nonNull(windowDetails) && Objects.nonNull(windowDetails.timeUnitValue) && windowDetails.timeUnitValue < 0) {
+      reporter.add(NEGATIVE_VALUE_ERROR, name, windowDetails.timeUnitValue, type);
     }
-
+  }
 
     private void checkObservationFilter(ObservationFilter filter, WarningReporter reporter, String name) {
+
         if (Objects.nonNull(filter)) {
             if (filter.priorDays < 0) {
                 reporter.add(NEGATIVE_VALUE_ERROR, name, filter.priorDays, "prior days");

src/main/java/org/ohdsi/circe/cohortdefinition/CohortExpressionQueryBuilder.java

@@ -20,8 +20,9 @@
 
 import com.fasterxml.jackson.annotation.JsonProperty;
 import com.fasterxml.jackson.databind.ObjectMapper;
-
-import java.util.*;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
 import java.util.stream.Collectors;
 import java.util.stream.IntStream;
 import org.apache.commons.lang3.StringUtils;
@@ -349,14 +350,14 @@ public String buildExpressionQuery(CohortExpression expression, BuildExpressionQ
     resultSql = StringUtils.replace(resultSql, "@finalCohortQuery", getFinalCohortQuery(expression.censorWindow));
 
     resultSql = StringUtils.replace(resultSql, "@cohort_end_unions", StringUtils.join(endDateSelects, "\nUNION ALL\n"));
-
-    if (!StringUtils.isEmpty(Integer.toString(expression.collapseSettings.eraPad)) && (expression.collapseSettings.eraPadUnit == null || IntervalUnit.DAY.getName().equals(expression.collapseSettings.eraPadUnit))) {
-      resultSql = StringUtils.replace(resultSql, "@eraconstructorpad", Integer.toString(expression.collapseSettings.eraPad));
-      resultSql = StringUtils.replace(resultSql, "@era_pad_unit", expression.collapseSettings.eraPadUnit);
-    } else {
-      resultSql = StringUtils.replace(resultSql, "@eraconstructorpad", Integer.toString(expression.collapseSettings.eraPadUnitValue));
-      resultSql = StringUtils.replace(resultSql, "@era_pad_unit", expression.collapseSettings.eraPadUnit);
+    if(expression.collapseSettings.eraPadUnit == null || expression.collapseSettings.eraPadUnit.equals("day")){
+      resultSql = StringUtils.replace(resultSql, "@eraPadValue", Integer.toString(expression.collapseSettings.eraPad));
+      resultSql = StringUtils.replace(resultSql, "@eraPadUnit", "day");
+    }else {
+      resultSql = StringUtils.replace(resultSql, "@eraPadValue", Integer.toString(expression.collapseSettings.eraPadValue));
+      resultSql = StringUtils.replace(resultSql, "@eraPadUnit", expression.collapseSettings.eraPadUnit);
     }
+
     resultSql = StringUtils.replace(resultSql, "@inclusionRuleTable", getInclusionRuleTableSql(expression));
     resultSql = StringUtils.replace(resultSql, "@inclusionImpactAnalysisByEventQuery", getInclusionAnalysisQuery("#qualified_events", 0));
     resultSql = StringUtils.replace(resultSql, "@inclusionImpactAnalysisByPersonQuery", getInclusionAnalysisQuery("#best_events", 1));
@@ -550,61 +551,64 @@ public String getWindowedCriteriaQuery(String sqlTemplate, WindowedCriteria crit
     Window startWindow = criteria.startWindow;
     String startIndexDateExpression = (startWindow.useIndexEnd != null && startWindow.useIndexEnd) ? "P.END_DATE" : "P.START_DATE";
     String startEventDateExpression = (startWindow.useEventEnd != null && startWindow.useEventEnd) ? "A.END_DATE" : "A.START_DATE";
-    if (startWindow.start.days != null && (startWindow.start.timeUnit == null || startWindow.start.timeUnit.equals(IntervalUnit.DAY.getName()))) {
-          startExpression = String.format("DATEADD(day,%d,%s)", startWindow.start.coeff * startWindow.start.days, startIndexDateExpression);
+    if (startWindow.start.days != null && (startWindow.start.timeUnit == null || IntervalUnit.DAY.getName().equals(startWindow.start.timeUnit))) {
+      startExpression = String.format("DATEADD(day,%d,%s)", startWindow.start.coeff * startWindow.start.days, startIndexDateExpression);
     } else if (startWindow.start.timeUnitValue != null) {
-          startExpression = String.format("DATEADD(%s,%d,%s)", startWindow.start.timeUnit, startWindow.start.coeff * startWindow.start.timeUnitValue, startIndexDateExpression);
+      startExpression = String.format("DATEADD(%s,%d,%s)", startWindow.start.timeUnit, startWindow.start.coeff * startWindow.start.timeUnitValue, startIndexDateExpression);
     } else {
-          startExpression = checkObservationPeriod ? (startWindow.start.coeff == -1 ? "P.OP_START_DATE" : "P.OP_END_DATE") : null;
+      startExpression = checkObservationPeriod ? (startWindow.start.coeff == -1 ? "P.OP_START_DATE" : "P.OP_END_DATE") : null;
     }
 
     if (startExpression != null) {
       clauses.add(String.format("%s >= %s", startEventDateExpression, startExpression));
     }
 
-    if (startWindow.end.days != null) {
-          endExpression = String.format("DATEADD(day,%d,%s)", startWindow.end.coeff * startWindow.end.days, startIndexDateExpression);
+    if (startWindow.end.days != null && (startWindow.end.timeUnit == null || IntervalUnit.DAY.getName().equals(startWindow.end.timeUnit))) {
+      endExpression = String.format("DATEADD(day,%d,%s)", startWindow.end.coeff * startWindow.end.days, startIndexDateExpression);
+    }else if(startWindow.end.timeUnitValue != null){
+      endExpression = String.format("DATEADD(%s,%d,%s)", startWindow.end.timeUnit, startWindow.end.coeff * startWindow.end.timeUnitValue, startIndexDateExpression);
     }
-    else if (startWindow.end.timeUnitValue != null) {
-          endExpression = String.format("DATEADD(%s,%d,%s)", startWindow.start.timeUnit, startWindow.end.coeff * startWindow.end.timeUnitValue, startIndexDateExpression);
-    } else {
-          endExpression = checkObservationPeriod ? (startWindow.end.coeff == -1 ? "P.OP_START_DATE" : "P.OP_END_DATE") : null;
+    else {
+      endExpression = checkObservationPeriod ? (startWindow.end.coeff == -1 ? "P.OP_START_DATE" : "P.OP_END_DATE") : null;
     }
 
     if (endExpression != null) {
       clauses.add(String.format("%s <= %s", startEventDateExpression, endExpression));
     }
 
-      // EndWindow
+    // EndWindow
     Window endWindow = criteria.endWindow;
 
     if (endWindow != null) {
       String endIndexDateExpression = (endWindow.useIndexEnd != null && endWindow.useIndexEnd) ? "P.END_DATE" : "P.START_DATE";
       // for backwards compatability, having a null endWindow.useIndexEnd means they SHOULD use the index end date.
       String endEventDateExpression = (endWindow.useEventEnd == null || endWindow.useEventEnd) ? "A.END_DATE" : "A.START_DATE";
-      if (endWindow.start.days != null) {
-          startExpression = String.format("DATEADD(day,%d,%s)", endWindow.start.coeff * endWindow.start.days, endIndexDateExpression);
-      } else if (endWindow.start.timeUnitValue != null) {
-             startExpression = String.format("DATEADD(%s,%d,%s)", endWindow.start.timeUnit, endWindow.start.coeff * endWindow.start.timeUnitValue, endIndexDateExpression);
-         } else {
-             startExpression = checkObservationPeriod ? (endWindow.start.coeff == -1 ? "P.OP_START_DATE" : "P.OP_END_DATE") : null;
-         }
-
-        if (startExpression != null) {
-          clauses.add(String.format("%s >= %s", endEventDateExpression, startExpression));
-        }
+      if (endWindow.start.days != null && (endWindow.start.timeUnit == null || IntervalUnit.DAY.getName().equals(endWindow.start.timeUnit))) {
+        startExpression = String.format("DATEADD(day,%d,%s)", endWindow.start.coeff * endWindow.start.days, endIndexDateExpression);
+      }else if(endWindow.start.timeUnitValue != null){
+        startExpression = String.format("DATEADD(%s,%d,%s)", endWindow.start.timeUnit, endWindow.start.coeff * endWindow.start.timeUnitValue, endIndexDateExpression);
+      }
+      else {
+        startExpression = checkObservationPeriod ? (endWindow.start.coeff == -1 ? "P.OP_START_DATE" : "P.OP_END_DATE") : null;
+      }
 
-      if (endWindow.end.days != null) {
-            endExpression = String.format("DATEADD(day,%d,%s)", endWindow.end.coeff * endWindow.end.days, endIndexDateExpression);
-      } else if (endWindow.end.timeUnitValue != null) {
-              endExpression = String.format("DATEADD(%s,%d,%s)", endWindow.start.timeUnit, endWindow.end.coeff * endWindow.end.timeUnitValue, endIndexDateExpression);
-        } else {
-              endExpression = checkObservationPeriod ? (endWindow.end.coeff == -1 ? "P.OP_START_DATE" : "P.OP_END_DATE") : null;
-        }
+      if (startExpression != null) {
+        clauses.add(String.format("%s >= %s", endEventDateExpression, startExpression));
+      }
 
-        if (endExpression != null) {
-          clauses.add(String.format("%s <= %s", endEventDateExpression, endExpression));
-        }
+      if (endWindow.end.days != null && (endWindow.end.timeUnit == null || IntervalUnit.DAY.getName().equals(endWindow.end.timeUnit))) {
+        endExpression = String.format("DATEADD(day,%d,%s)", endWindow.end.coeff * endWindow.end.days, endIndexDateExpression);
+      }
+      else if(endWindow.end.timeUnitValue != null){
+        endExpression = String.format("DATEADD(%s,%d,%s)", endWindow.end.timeUnit, endWindow.end.coeff * endWindow.end.timeUnitValue, endIndexDateExpression);
+      }
+      else {
+        endExpression = checkObservationPeriod ? (endWindow.end.coeff == -1 ? "P.OP_START_DATE" : "P.OP_END_DATE") : null;
+      }
+
+      if (endExpression != null) {
+        clauses.add(String.format("%s <= %s", endEventDateExpression, endExpression));
+      }
     }
 
     // RestrictVisit
@@ -618,7 +622,7 @@ else if (startWindow.end.timeUnitValue != null) {
     return query;
   }
 
-    public String getWindowedCriteriaQuery(WindowedCriteria criteria, String eventTable) {
+  public String getWindowedCriteriaQuery(WindowedCriteria criteria, String eventTable) {
     String query = getWindowedCriteriaQuery(WINDOWED_CRITERIA_TEMPLATE, criteria, eventTable, null);
     return query;
   }
@@ -776,7 +780,7 @@ private String getDateFieldForOffsetStrategy(DateOffsetStrategy.DateField dateFi
   @Override
   public String getStrategySql(DateOffsetStrategy strat, String eventTable) {
     String strategySql = StringUtils.replace(DATE_OFFSET_STRATEGY_TEMPLATE, "@eventTable", eventTable);
-    if (strat.offsetUnit == null || strat.offsetUnit.equals(IntervalUnit.DAY.getName())) {
+    if (strat.offsetUnit == null || IntervalUnit.DAY.getName().equals(strat.offsetUnit)) {
       strategySql = StringUtils.replace(strategySql, "@offsetUnitValue", Integer.toString(strat.offset));
       strategySql = StringUtils.replace(strategySql, "@offsetUnit", "day");
     } else {
@@ -796,28 +800,37 @@ public String getStrategySql(CustomEraStrategy strat, String eventTable) {
     }
 
     String drugExposureEndDateExpression = DEFAULT_DRUG_EXPOSURE_END_DATE_EXPRESSION;
-    if (strat.daysSupplyOverride != null) {
+    if (strat.daysSupplyOverride != null && IntervalUnit.DAY.getName().equals(strat.gapUnit)) {
       drugExposureEndDateExpression = String.format("DATEADD(day,%d,DRUG_EXPOSURE_START_DATE)", strat.daysSupplyOverride);
+    }else if(strat.daysSupplyOverride != null && IntervalUnit.HOUR.getName().equals(strat.gapUnit)){
+      drugExposureEndDateExpression = String.format("DATEADD(hour,%d,DRUG_EXPOSURE_START_DATE)", strat.daysSupplyOverride);
+    }else if(strat.daysSupplyOverride != null && IntervalUnit.MINUTE.getName().equals(strat.gapUnit)){
+      drugExposureEndDateExpression = String.format("DATEADD(minute,%d,DRUG_EXPOSURE_START_DATE)", strat.daysSupplyOverride);
+    }else if(strat.daysSupplyOverride != null && IntervalUnit.SECOND.getName().equals(strat.gapUnit)){
+      drugExposureEndDateExpression = String.format("DATEADD(second,%d,DRUG_EXPOSURE_START_DATE)", strat.daysSupplyOverride);
     }
     String strategySql = StringUtils.replace(CUSTOM_ERA_STRATEGY_TEMPLATE, "@eventTable", eventTable);
     strategySql = StringUtils.replace(strategySql, "@drugCodesetId", strat.drugCodesetId.toString());
-    if (IntervalUnit.DAY.getName().equals(strat.gapUnit)) {
+    if ("day".equals(strat.gapUnit) || strat.gapUnit == null) {
       strategySql = StringUtils.replace(strategySql, "@gapUnitValue", Integer.toString(strat.gapDays));
-    } else {
+      strategySql = StringUtils.replace(strategySql, "@gapUnit", "day");
+    }else {
       strategySql = StringUtils.replace(strategySql, "@gapUnitValue", Integer.toString(strat.gapUnitValue));
+      strategySql = StringUtils.replace(strategySql, "@gapUnit", strat.gapUnit);
+
     }
-    strategySql = StringUtils.replace(strategySql, "@gapUnit", strat.gapUnit);
-    if (IntervalUnit.DAY.getName().equals(strat.offsetUnit)) {
+    if("day".equals(strat.offsetUnit) || strat.offsetUnit == null){
       strategySql = StringUtils.replace(strategySql, "@offsetUnitValue", Integer.toString(strat.offset));
-    } else {
+      strategySql = StringUtils.replace(strategySql, "@offsetUnit", "day");
+    }else {
       strategySql = StringUtils.replace(strategySql, "@offsetUnitValue", Integer.toString(strat.offsetUnitValue));
+      strategySql = StringUtils.replace(strategySql, "@offsetUnit", strat.offsetUnit);
     }
-    strategySql = StringUtils.replace(strategySql, "@offsetUnit", strat.offsetUnit);
+
     strategySql = StringUtils.replace(strategySql, "@drugExposureEndDateExpression", drugExposureEndDateExpression);
 
     return strategySql;
   }
 
 // </editor-fold>
-
 }